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When a lookup contains a lot of entries, it is recommended (and sometimes even mandatory) to create multiple subtables to keep things organized. The Subtable Manager allows you to add, remove, rename and move subtables.
Just as with normal lookups, the order in which subtables appear controls how they are processed.
Note: There are technical limitations to how many items can be stored in each subtable. When a font is exported, FontCreator will break up subtables into several separate subtables if necessary. We do however recommend splitting larger lookups into several subtables yourself to keep your items organized.